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This page was generated on 2024-12-23 11:45 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1456/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.1.3  (landing page)
Vincent Carey
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: e973100
git_last_commit_date: 2024-12-04 13:09:36 -0500 (Wed, 04 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for ontoProc on kjohnson3

To the developers/maintainers of the ontoProc package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ontoProc
Version: 2.1.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_2.1.3.tar.gz
StartedAt: 2024-12-22 20:36:05 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 20:41:32 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 327.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ontoProc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ontoProc_2.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* this is package ‘ontoProc’ version ‘2.1.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ontoProc’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 10.5Mb
  sub-directories of 1Mb or more:
    app       1.9Mb
    data      1.8Mb
    ontoRda   2.8Mb
    owl       3.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘ontologyPlot:::remove_uninformative_terms’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CLfeat : prupdate: no visible binding for global variable ‘PROSYM’
CLfeat : prupdate: no visible binding for global variable ‘PRID’
CLfeat : prupdate: no visible binding for global variable ‘SYMBOL’
ctmarks : server: no visible binding for global variable ‘text’
ctmarks : server: no visible binding for global variable ‘packDesc2022’
ctmarks : server: no visible binding for global variable ‘packDesc2021’
ctmarks: no visible binding for global variable ‘cumu’
dropStop: no visible binding for global variable ‘stopWords’
getOnto: no visible binding for global variable ‘rdatadateadded’
getOnto: no visible binding for global variable ‘title’
getOnto: no visible binding for global variable ‘description’
ldfToTerm: no visible binding for global variable ‘PROSYM’
sym2CellOnto: no visible binding for global variable ‘PROSYM’
sym2CellOnto: no visible binding for global variable ‘SYMBOL’
Undefined global functions or variables:
  PRID PROSYM SYMBOL cumu description packDesc2021 packDesc2022
  rdatadateadded stopWords text title
Consider adding
  importFrom("graphics", "text", "title")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  findCommonAncestors.Rd: graph, DataFrame-class, List-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in Rd file 'plot.owlents.Rd':
  ‘plot.owlents’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
sym2CellOnto                     20.249  0.437  24.364
CLfeats                          13.022  0.480  14.533
siblings_TAG                     11.829  0.506  14.925
nomenCheckup                      6.789  0.229  10.498
owl2cache                         6.321  0.192   7.177
labels.owlents                    5.839  0.245   6.998
getLeavesFromTerm                 5.431  0.198   5.810
fastGrep                          5.167  0.234   5.648
cleanCLOnames                     4.939  0.177   5.440
ancestors                         4.879  0.179   4.670
ontoDiff                          4.009  0.325   6.541
make_graphNEL_from_ontology_plot  4.077  0.208   6.679
mapOneNaive                       3.518  0.177   5.489
search_labels                     0.123  0.015  27.723
bioregistry_ols_resources         0.019  0.008   6.372
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck/00check.log’
for details.


Installation output

ontoProc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ontoProc
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ontoProc’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ontoProc)

Tests output

ontoProc.Rcheck/tests/test.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> library(ontoProc)
Loading required package: ontologyIndex
> library(testthat)
> 
> test_check("ontoProc")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 48.345   3.915  53.738 

Example timings

ontoProc.Rcheck/ontoProc-Ex.timings

nameusersystemelapsed
CLfeats13.022 0.48014.533
PROSYM0.1220.0020.125
TermSet-class3.1830.1513.505
allGOterms0.0590.0010.061
ancestors4.8790.1794.670
ancestors_names1.1470.0291.192
bioregistry_ols_resources0.0190.0086.372
cellTypeToGO0.9820.0411.025
children_names1.1490.0151.167
cleanCLOnames4.9390.1775.440
common_classes3.7150.2934.197
ctmarks000
cyclicSigset0.0020.0000.002
demoApp0.0000.0000.001
dropStop0.0010.0000.002
fastGrep5.1670.2345.648
findCommonAncestors3.0940.1933.461
getLeavesFromTerm5.4310.1985.810
getOnto3.1600.2253.560
humrna0.0030.0010.003
labels.owlents5.8390.2456.998
ldfToTerms1.0530.0191.072
liberalMap2.7500.1723.407
makeSelectInput0.0010.0000.000
make_graphNEL_from_ontology_plot4.0770.2086.679
mapOneNaive3.5180.1775.489
minicorpus0.0010.0010.001
nomenCheckup 6.789 0.22910.498
ontoDiff4.0090.3256.541
onto_plot22.8040.1743.234
onto_roots000
owl2cache6.3210.1927.177
packDesc20190.0010.0000.002
packDesc20210.0010.0010.002
packDesc20220.0010.0010.001
packDesc20230.0000.0020.003
parents0.970.010.98
plot.owlents1.2750.0141.290
recognizedPredicates000
search_labels 0.123 0.01527.723
secLevGen3.0610.1633.624
selectFromMap2.9410.1573.329
setup_entities1.0830.0121.095
setup_entities20.1210.0040.125
seur3kTab0.0010.0000.002
siblings_TAG11.829 0.50614.925
stopWords0.0010.0010.001
subclasses1.2580.0162.131
sym2CellOnto20.249 0.43724.364
valid_ontonames0.0010.0000.000